samtools sort

samtools sort

1

I am transforming sam files to bam, to facilitate their ordering I use this command,

% cd /Volumes/GENOMA/BWA 
% samtools sort -n -O V350019555_L03_B5GHUMqcnrRAABA-551.sam | samtools fixmate -m -O bam V350019555_L03_B5GHUMqcnrRAABA-551.bam

but it gives me the following error,

As elsewhere in samtools, use ‘-‘ as the filename for stdin/stdout. The input
file must be grouped by read name (e.g. sorted by name). Coordinated sorted
input is not accepted.
(base) javier@iMac-de-JAVIER BWA %

I use the version of samtools 1.10


sort


ordering

• 40 views

samtools sort -n -l 0  -O BAM  -T tmp in.sam |  samtools fixmate -m -O BAM  -  out.bam


Login
before adding your answer.

Read more here: Source link